Mutagenetix > Incidental Mutation

Incidental Mutation 'R2184:Trmt2a'

237393

Institutional Source

Beutler Lab

Gene Symbol

Trmt2a

Ensembl Gene

ENSMUSG00000022721

Gene Name

TRM2 tRNA methyltransferase 2A

Synonyms

Htf9c

MMRRC Submission

040186-MU

Accession Numbers

Is this an essential gene?

Non essential (E-score: 0.000) question?

Stock #

R2184 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

18248679-18254772 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 18252995 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Arginine to Tryptophan at position 531 (R531W)

Ref Sequence

ENSEMBL: ENSMUSP00000111303 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000009321] [ENSMUST00000052325] [ENSMUST00000100099] [ENSMUST00000115633] [ENSMUST00000115640] [ENSMUST00000115645] [ENSMUST00000128045] [ENSMUST00000140206] [ENSMUST00000231509]

AlphaFold

Q8BNV1

Predicted Effect

probably benign
Transcript: ENSMUST00000009321

SMART Domains

Protein: ENSMUSP00000009321
Gene: ENSMUSG00000022718

Domain	Start	End	E-Value	Type
low complexity region	165	176	N/A	INTRINSIC
WW	302	334	7.26e-6	SMART
low complexity region	411	421	N/A	INTRINSIC
DSRM	512	577	5.68e-10	SMART
DSRM	620	685	8.26e-1	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000052325

SMART Domains

Protein: ENSMUSP00000055288
Gene: ENSMUSG00000005732

Domain	Start	End	E-Value	Type
RanBD	1	108	4.92e-46	SMART
coiled coil region	123	153	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000059696

Predicted Effect

probably benign
Transcript: ENSMUST00000100099
AA Change: R531W

PolyPhen 2 Score 0.065 (Sensitivity: 0.94; Specificity: 0.84)

SMART Domains

Protein: ENSMUSP00000111303
Gene: ENSMUSG00000022721
AA Change: R531W

Domain	Start	End	E-Value	Type
low complexity region	35	44	N/A	INTRINSIC
RRM	64	132	1.37e-2	SMART
coiled coil region	171	195	N/A	INTRINSIC
Pfam:tRNA_U5-meth_tr	380	579	1.2e-20	PFAM
Pfam:PCMT	386	482	1.1e-8	PFAM
Pfam:MTS	389	489	6.2e-9	PFAM
Pfam:Methyltransf_4	397	497	4.2e-7	PFAM
Pfam:Methyltransf_31	420	546	6.2e-15	PFAM
Pfam:Methyltransf_18	422	523	9.3e-11	PFAM
Pfam:Methyltransf_26	423	538	5.3e-12	PFAM
Pfam:Methyltransf_25	426	511	3.5e-8	PFAM
Pfam:Methyltransf_11	427	487	5.6e-6	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000115633

SMART Domains

Protein: ENSMUSP00000111296
Gene: ENSMUSG00000022718

Domain	Start	End	E-Value	Type
low complexity region	165	176	N/A	INTRINSIC
WW	302	334	7.26e-6	SMART
low complexity region	411	421	N/A	INTRINSIC
DSRM	512	577	5.68e-10	SMART
DSRM	620	685	8.26e-1	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000115640
AA Change: R531W

PolyPhen 2 Score 0.017 (Sensitivity: 0.95; Specificity: 0.80)

SMART Domains

Protein: ENSMUSP00000111304
Gene: ENSMUSG00000022721
AA Change: R531W

Domain	Start	End	E-Value	Type
low complexity region	35	44	N/A	INTRINSIC
RRM	64	132	1.37e-2	SMART
coiled coil region	171	195	N/A	INTRINSIC
Pfam:tRNA_U5-meth_tr	380	579	2.6e-20	PFAM
Pfam:PCMT	386	482	3.4e-9	PFAM
Pfam:MTS	392	489	1e-7	PFAM
Pfam:Cons_hypoth95	405	542	2.7e-7	PFAM
Pfam:Methyltransf_31	420	547	2.1e-15	PFAM
Pfam:Methyltransf_18	422	526	2.9e-12	PFAM
Pfam:Methyltransf_4	423	499	2.6e-7	PFAM
Pfam:Methyltransf_25	426	511	1.3e-8	PFAM
Pfam:Methyltransf_11	427	489	3.6e-8	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000115645

SMART Domains

Protein: ENSMUSP00000111309
Gene: ENSMUSG00000005732

Domain	Start	End	E-Value	Type
RanBD	27	158	3.33e-75	SMART
low complexity region	183	202	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000123073

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000127239

Predicted Effect

probably benign
Transcript: ENSMUST00000128045

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000131211

Predicted Effect

probably benign
Transcript: ENSMUST00000140206
AA Change: R492W

PolyPhen 2 Score 0.019 (Sensitivity: 0.95; Specificity: 0.80)

SMART Domains

Protein: ENSMUSP00000121216
Gene: ENSMUSG00000022721
AA Change: R492W

Domain	Start	End	E-Value	Type
low complexity region	35	44	N/A	INTRINSIC
RRM	64	132	1.37e-2	SMART
coiled coil region	171	195	N/A	INTRINSIC
Pfam:tRNA_U5-meth_tr	383	481	3.7e-8	PFAM
Pfam:PCMT	386	481	1.5e-6	PFAM
Pfam:MTS	389	493	2.5e-7	PFAM
Pfam:Methyltransf_31	420	491	1.5e-9	PFAM
Pfam:Methyltransf_18	422	508	4.1e-8	PFAM
Pfam:Methyltransf_26	423	523	3.1e-9	PFAM

Predicted Effect

unknown
Transcript: ENSMUST00000145112
AA Change: R268W

SMART Domains

Protein: ENSMUSP00000117026
Gene: ENSMUSG00000022721
AA Change: R268W

Domain	Start	End	E-Value	Type
Pfam:PCMT	118	220	4.2e-7	PFAM
Pfam:tRNA_U5-meth_tr	118	280	4e-16	PFAM
Pfam:MTS	129	229	5.4e-6	PFAM
Pfam:Cons_hypoth95	143	277	6.5e-5	PFAM
Pfam:PrmA	146	234	2e-4	PFAM
Pfam:Ubie_methyltran	148	223	1e-4	PFAM
Pfam:Methyltransf_31	158	271	6.1e-14	PFAM
Pfam:Methyltransf_18	160	263	8.3e-11	PFAM
Pfam:Methyltransf_4	161	237	7.1e-5	PFAM
Pfam:Methyltransf_26	161	274	2e-6	PFAM
Pfam:Methyltransf_25	164	251	5.2e-7	PFAM
Pfam:Methyltransf_11	165	227	9.4e-7	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000147273

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000152033

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000153292

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000144536

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000134035

Predicted Effect

probably benign
Transcript: ENSMUST00000232293

Predicted Effect

probably benign
Transcript: ENSMUST00000232144

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000232342

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000232015

Predicted Effect

probably benign
Transcript: ENSMUST00000231509

Coding Region Coverage

1x: 99.2%
3x: 98.7%
10x: 97.4%
20x: 95.4%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is of unknown function. However, it is orthologous to the mouse Trmt2a gene and contains an RNA methyltransferase domain. Expression of this gene varies during the cell cycle, with aberrant expression being a possible biomarker in certain breast cancers. Several transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Apr 2012]

Allele List at MGI

Other mutations in this stock

Total: 78 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700088E04Rik	T	C	15: 79,135,189	R184G	probably damaging	Het
2300002M23Rik	C	A	17: 35,568,218	A151E	probably benign	Het
A930011G23Rik	C	T	5: 99,232,369	R339Q	possibly damaging	Het
Abcd2	T	C	15: 91,191,439	Y57C	probably benign	Het
Adprhl1	A	G	8: 13,242,559	V244A	probably benign	Het
Agl	T	C	3: 116,780,777	N753D	probably benign	Het
Amotl1	T	A	9: 14,575,390	M440L	probably benign	Het
Angpt2	A	G	8: 18,692,116	Y475H	probably benign	Het
Angpt4	A	T	2: 151,938,954	H374L	probably damaging	Het
Ank1	A	T	8: 23,109,254	T801S	probably damaging	Het
Ap5m1	G	T	14: 49,086,295	A481S	probably damaging	Het
AY358078	G	T	14: 51,825,988	G364W	probably damaging	Het
C4b	C	A	17: 34,737,702	A641S	probably benign	Het
Capn13	T	C	17: 73,365,948	Y120C	probably damaging	Het
Cbx6	T	C	15: 79,828,561	T222A	probably benign	Het
Cckar	T	C	5: 53,702,912	T192A	probably damaging	Het
Cdc42bpb	T	C	12: 111,296,044	D30G	probably damaging	Het
Cdk18	A	G	1: 132,115,952	Y385H	probably damaging	Het
Cep170	A	T	1: 176,756,976	D612E	probably benign	Het
Dennd4b	G	T	3: 90,275,540	R888L	probably damaging	Het
Egf	A	T	3: 129,723,358	C373*	probably null	Het
Fam208a	T	A	14: 27,466,184	N862K	possibly damaging	Het
Gabrb2	T	C	11: 42,421,428		probably null	Het
Gle1	G	T	2: 29,949,018	A482S	probably damaging	Het
Gm10644	T	C	8: 83,933,627	T30A	possibly damaging	Het
Gmnn	A	G	13: 24,753,723	Y95H	probably damaging	Het
Hectd3	T	A	4: 117,000,903	S643T	possibly damaging	Het
Hoga1	A	G	19: 42,061,391	Y225C	probably damaging	Het
Hook3	T	C	8: 26,118,983	E11G	probably benign	Het
Hsd17b1	C	A	11: 101,078,531	S30R	probably benign	Het
Htr3b	G	A	9: 48,947,244	P112S	probably damaging	Het
Iqch	T	A	9: 63,525,069	D348V	probably damaging	Het
Irgm2	A	T	11: 58,220,428	N327I	probably benign	Het
Itgb4	T	C	11: 115,979,624	I93T	probably damaging	Het
Lamb2	T	C	9: 108,480,553	F92L	probably damaging	Het
Lats2	T	C	14: 57,691,559	H953R	probably damaging	Het
Lrp1b	T	C	2: 40,730,702	E3588G	probably benign	Het
March1	A	G	8: 66,387,423	E286G	probably benign	Het
Mc2r	G	T	18: 68,408,125	F32L	probably benign	Het
Mink1	C	T	11: 70,603,797	T268M	probably damaging	Het
Mta1	G	A	12: 113,130,195		probably null	Het
Muc5b	C	A	7: 141,858,864	S1849*	probably null	Het
Myh15	A	G	16: 49,137,511	E897G	probably damaging	Het
Nobox	T	C	6: 43,304,885	Q418R	possibly damaging	Het
Obsl1	G	T	1: 75,502,217	Q626K	probably benign	Het
Olfr1058	G	A	2: 86,386,145	T91I	probably benign	Het
Olfr1137	G	A	2: 87,711,205	R234C	probably damaging	Het
Olfr1502	A	G	19: 13,862,035	I81V	probably benign	Het
Olfr225	T	A	11: 59,613,138	M58K	probably damaging	Het
Olfr340	A	G	2: 36,453,034	T150A	probably benign	Het
Olfr538	T	C	7: 140,574,402	V83A	probably benign	Het
Olfr749	A	G	14: 50,736,602	S187P	probably damaging	Het
Pald1	C	T	10: 61,347,136	A345T	possibly damaging	Het
Pde8b	G	A	13: 95,026,215	P800S	probably damaging	Het
Pgm2l1	G	A	7: 100,268,155	C493Y	possibly damaging	Het
Pias3	A	G	3: 96,702,221	S311G	possibly damaging	Het
Pkhd1l1	A	G	15: 44,499,296	N573D	possibly damaging	Het
Pla2g16	A	G	19: 7,579,218	D128G	probably damaging	Het
Plxnc1	T	G	10: 94,944,269	S104R	probably damaging	Het
Pofut2	T	A	10: 77,267,225	F179I	probably damaging	Het
Prkcsh	T	A	9: 22,004,732	C112S	probably damaging	Het
Prss32	G	A	17: 23,859,323	A328T	probably benign	Het
Ptgir	G	T	7: 16,908,783	R103L	probably damaging	Het
Ptpn5	G	A	7: 47,088,602	S244F	probably damaging	Het
Rnpepl1	G	A	1: 92,916,823	V346I	probably benign	Het
Sh3rf1	T	A	8: 61,372,654	V561D	probably damaging	Het
Slc22a19	A	T	19: 7,709,661	Y160N	probably benign	Het
Sorbs3	A	G	14: 70,191,431		probably null	Het
Sostdc1	T	G	12: 36,317,296	I157S	probably damaging	Het
Svil	G	T	18: 5,099,534	R1777L	probably damaging	Het
Svil	A	T	18: 5,099,615	E1804V	probably damaging	Het
Thbs4	A	G	13: 92,774,794	S294P	probably benign	Het
Tle2	A	G	10: 81,590,277	Y750C	probably damaging	Het
Tmcc3	T	C	10: 94,582,306	L312P	probably damaging	Het
Tnip2	TCTCCT	TCT	5: 34,499,613		probably benign	Het
Tnpo2	T	A	8: 85,053,846	M734K	probably benign	Het
Ubn2	C	T	6: 38,484,094	R483W	probably damaging	Het
Zc3hav1	T	A	6: 38,307,408	Y924F	probably damaging	Het

Other mutations in Trmt2a

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00088:Trmt2a	APN	16	18249487	missense	probably benign
R0050:Trmt2a	UTSW	16	18250843	missense	probably damaging	1.00
R0050:Trmt2a	UTSW	16	18250843	missense	probably damaging	1.00
R0377:Trmt2a	UTSW	16	18249703	missense	possibly damaging	0.68
R0699:Trmt2a	UTSW	16	18249529	missense	probably benign	0.01
R1034:Trmt2a	UTSW	16	18249709	missense	probably damaging	1.00
R1114:Trmt2a	UTSW	16	18250440	unclassified	probably benign
R1882:Trmt2a	UTSW	16	18249894	missense	possibly damaging	0.88
R1911:Trmt2a	UTSW	16	18251206	missense	probably benign	0.01
R3853:Trmt2a	UTSW	16	18251191	missense	possibly damaging	0.94
R4427:Trmt2a	UTSW	16	18249229	unclassified	probably benign
R4737:Trmt2a	UTSW	16	18251286	unclassified	probably benign
R4896:Trmt2a	UTSW	16	18252929	missense	probably damaging	0.99
R4903:Trmt2a	UTSW	16	18249554	nonsense	probably null
R4964:Trmt2a	UTSW	16	18249554	nonsense	probably null
R4966:Trmt2a	UTSW	16	18249554	nonsense	probably null
R5216:Trmt2a	UTSW	16	18252184	missense	probably benign	0.22
R5452:Trmt2a	UTSW	16	18250950	missense	probably damaging	1.00
R5837:Trmt2a	UTSW	16	18249462	unclassified	probably benign
R6555:Trmt2a	UTSW	16	18253203	missense	probably benign	0.03
R6670:Trmt2a	UTSW	16	18250477	missense	possibly damaging	0.57
R7064:Trmt2a	UTSW	16	18253004	missense	probably damaging	0.99
R7718:Trmt2a	UTSW	16	18250623	missense	probably benign	0.16
R8302:Trmt2a	UTSW	16	18249949	missense	probably damaging	1.00
R8463:Trmt2a	UTSW	16	18251175	missense	probably damaging	1.00
R9120:Trmt2a	UTSW	16	18249858	missense	probably damaging	1.00
R9186:Trmt2a	UTSW	16	18251169	missense	probably benign	0.00
R9487:Trmt2a	UTSW	16	18250950	missense	probably damaging	1.00
R9710:Trmt2a	UTSW	16	18252177	nonsense	probably null

Predicted Primers

PCR Primer
(F):5'- ACTTGTAGCTGTTCTAGACCCAC -3'
(R):5'- ATCTCACAGTGCGGAGTCTG -3'

Sequencing Primer
(F):5'- TGTTCTAGACCCACCACGG -3'
(R):5'- CGGAGTCTGTGGGAACAGGTC -3'

Posted On

2014-10-02